Cltrn (collectrin, amino acid transport regulator) - Rat Genome Database

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Gene: Cltrn (collectrin, amino acid transport regulator) Mus musculus
Analyze
Symbol: Cltrn
Name: collectrin, amino acid transport regulator
RGD ID: 1623240
MGI Page MGI
Description: Enables protein homodimerization activity. Acts upstream of or within positive regulation of amino acid transport. Located in brush border membrane. Is expressed in genitourinary system. Orthologous to human CLTRN (collectrin, amino acid transport regulator).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 0610008J07Rik; coll; collectrin; kidney-specific membrane protein; NX-17; NX1; NX17; NX=1; Tmem27; transmembrane protein 27
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X162,873,183 - 162,901,855 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX162,871,826 - 162,901,856 (+)EnsemblGRCm39 Ensembl
GRCm38X164,090,187 - 164,118,859 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX164,088,830 - 164,118,860 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X160,528,119 - 160,556,791 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X159,434,292 - 159,462,964 (+)NCBIMGSCv36mm8
CeleraX147,304,655 - 147,333,264 (+)NCBICelera
Cytogenetic MapXF5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
brush border membrane  (IDA)
cytoplasm  (ISO)
membrane  (IEA)
plasma membrane  (IBA,IDA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10432394   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11278314   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15172686   PMID:15489334   PMID:16141072  
PMID:16141073   PMID:16330323   PMID:16330324   PMID:16985211   PMID:17167413   PMID:17693757   PMID:18287559   PMID:19185582   PMID:19246514   PMID:19478081   PMID:19715677   PMID:20003319  
PMID:20562862   PMID:21343540   PMID:21677750   PMID:21814048   PMID:21873635   PMID:21907142   PMID:21947380   PMID:22837003   PMID:24048198   PMID:26240152   PMID:26901059   PMID:28159899  
PMID:32179912   PMID:33737325   PMID:36264884   PMID:36611813  


Genomics

Comparative Map Data
Cltrn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X162,873,183 - 162,901,855 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX162,871,826 - 162,901,856 (+)EnsemblGRCm39 Ensembl
GRCm38X164,090,187 - 164,118,859 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX164,088,830 - 164,118,860 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X160,528,119 - 160,556,791 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X159,434,292 - 159,462,964 (+)NCBIMGSCv36mm8
CeleraX147,304,655 - 147,333,264 (+)NCBICelera
Cytogenetic MapXF5NCBI
CLTRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X15,627,318 - 15,675,644 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX15,627,318 - 15,675,012 (-)EnsemblGRCh38hg38GRCh38
GRCh37X15,645,441 - 15,682,928 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X15,555,372 - 15,593,075 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X15,405,107 - 15,442,811NCBI
CeleraX19,760,931 - 19,798,641 (-)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX13,399,991 - 13,438,249 (-)NCBIHuRef
CHM1_1X15,676,401 - 15,714,121 (-)NCBICHM1_1
T2T-CHM13v2.0X15,210,303 - 15,247,770 (-)NCBIT2T-CHM13v2.0
Cltrn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X30,361,967 - 30,395,264 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX30,361,967 - 30,395,349 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX31,394,873 - 31,428,148 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X34,831,861 - 34,865,158 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X31,019,084 - 31,052,359 (-)NCBIRnor_WKY
Rnor_6.0X32,118,082 - 32,153,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX32,118,054 - 32,153,794 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X32,490,603 - 32,522,780 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X51,118,665 - 51,149,768 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X51,172,133 - 51,203,237 (-)NCBI
CeleraX30,705,756 - 30,738,867 (-)NCBICelera
Cytogenetic MapXq14NCBI
Cltrn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555192,522,155 - 2,570,972 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555192,522,154 - 2,569,722 (+)NCBIChiLan1.0ChiLan1.0
CLTRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X17,431,727 - 17,469,290 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X8,255,666 - 8,293,354 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X15,537,112 - 15,574,842 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX15,535,069 - 15,575,268 (-)Ensemblpanpan1.1panPan2
CLTRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X11,863,479 - 11,908,361 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX11,798,839 - 11,900,594 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX11,770,083 - 11,786,549 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X11,824,506 - 11,859,272 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX11,825,149 - 11,861,692 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X11,887,674 - 11,922,326 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X11,881,588 - 11,916,356 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X11,907,346 - 11,941,809 (-)NCBIUU_Cfam_GSD_1.0
Cltrn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X5,040,429 - 5,129,055 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364705,040,795 - 5,124,192 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364705,040,831 - 5,124,611 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLTRN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX12,183,796 - 12,224,964 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X12,183,793 - 12,215,474 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X13,279,802 - 13,292,665 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLTRN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X14,103,046 - 14,154,936 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX14,102,497 - 14,154,123 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605615,936,757 - 15,975,408 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cltrn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624829412,532 - 446,938 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624829412,797 - 447,076 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cltrn
766 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:450
Count of miRNA genes:277
Interacting mature miRNAs:314
Transcripts:ENSMUST00000015545, ENSMUST00000112280, ENSMUST00000141818
Prediction methods:Miranda, Pita, Pita,Targetscan, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558900Bw3_mbody weight QTL 3 (mouse)Not determinedX133540040165298595Mouse
10401118Pgia39_mproteoglycan induced arthritis 39 (mouse)Not determinedX144474380169476592Mouse
1302000Pgia25_mproteoglycan induced arthritis 2 (mouse)Not determinedX144474380169476592Mouse
12738421Lfibq17_mliver fibrosis QTL 17 (mouse)X148148453164945064Mouse
1357619Obsty5_mobesity 5 (mouse)Not determinedX160212893164149284Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000015545   ⟹   ENSMUSP00000015545
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX162,873,183 - 162,901,855 (+)Ensembl
GRCm38.p6 EnsemblX164,090,187 - 164,118,859 (+)Ensembl
RefSeq Acc Id: ENSMUST00000112280   ⟹   ENSMUSP00000107899
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX162,871,826 - 162,901,856 (+)Ensembl
GRCm38.p6 EnsemblX164,088,830 - 164,118,860 (+)Ensembl
RefSeq Acc Id: ENSMUST00000141818   ⟹   ENSMUSP00000123629
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX162,875,185 - 162,901,210 (+)Ensembl
GRCm38.p6 EnsemblX164,092,189 - 164,118,214 (+)Ensembl
RefSeq Acc Id: NM_001313719   ⟹   NP_001300648
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39X162,875,185 - 162,901,855 (+)NCBI
GRCm38X164,092,189 - 164,118,859 (+)NCBI
Sequence:
RefSeq Acc Id: NM_020626   ⟹   NP_065651
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39X162,873,183 - 162,901,855 (+)NCBI
GRCm38X164,090,187 - 164,118,859 (+)NCBI
MGSCv37X160,528,119 - 160,556,791 (+)RGD
CeleraX147,304,655 - 147,333,264 (+)RGD
cM MapX ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_065651   ⟸   NM_020626
- Peptide Label: isoform 1 precursor
- UniProtKB: Q3UFF6 (UniProtKB/Swiss-Prot),   Q9ESG4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001300648   ⟸   NM_001313719
- Peptide Label: isoform 2
- UniProtKB: Q9ESG4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000015545   ⟸   ENSMUST00000015545
RefSeq Acc Id: ENSMUSP00000107899   ⟸   ENSMUST00000112280
RefSeq Acc Id: ENSMUSP00000123629   ⟸   ENSMUST00000141818
Protein Domains
Collectrin   Collectrin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9ESG4-F1-model_v2 AlphaFold Q9ESG4 1-222 view protein structure

Promoters
RGD ID:6846457
Promoter ID:MM_KWN:62681
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:ENSMUST00000112280
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36X160,526,801 - 160,527,301 (+)MPROMDB
RGD ID:6846458
Promoter ID:MM_KWN:62682
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:ENSMUST00000112278,   NM_020626
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36X160,527,801 - 160,528,301 (+)MPROMDB
RGD ID:6846460
Promoter ID:MM_KWN:62683
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:OTTMUST00000046592
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36X160,530,001 - 160,530,502 (+)MPROMDB
RGD ID:13681806
Promoter ID:EPDNEW_M25052
Type:initiation region
Name:Tmem27_1
Description:Mus musculus transmembrane protein 27 , transcript variant 2,mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38X164,090,243 - 164,090,303EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1926234 AgrOrtholog
Ensembl Genes ENSMUSG00000015401 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000015545 ENTREZGENE
  ENSMUSP00000015545.4 UniProtKB/Swiss-Prot
  ENSMUSP00000107899.2 UniProtKB/Swiss-Prot
  ENSMUSP00000123629.2 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000015545 ENTREZGENE
  ENSMUST00000015545.10 UniProtKB/Swiss-Prot
  ENSMUST00000112280.8 UniProtKB/Swiss-Prot
  ENSMUST00000141818.2 UniProtKB/TrEMBL
InterPro Collectrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collectrin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:57394 UniProtKB/Swiss-Prot
MGD MGI:1926234 ENTREZGENE
NCBI Gene 57394 ENTREZGENE
PANTHER COLLECTRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR46884 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Collectrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cltrn PhenoGen
PROSITE COLLECTRIN_LIKE UniProtKB/Swiss-Prot
UniProt A2AHZ5_MOUSE UniProtKB/TrEMBL
  CLTRN_MOUSE UniProtKB/Swiss-Prot
  Q3UFF6 ENTREZGENE
  Q9ESG4 ENTREZGENE
UniProt Secondary Q3UFF6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-06-05 Cltrn  collectrin, amino acid transport regulator  Tmem27  transmembrane protein 27  Symbol and/or name change 5135510 APPROVED